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- PDB-6qju: Crystal structure of human Bromodomain containing protein 3 (BRD3... -

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Basic information

Entry
Database: PDB / ID: 6qju
TitleCrystal structure of human Bromodomain containing protein 3 (BRD3) in complex with 3-bromo-1H-indazol-5-amine
ComponentsBromodomain-containing protein 3
KeywordsSIGNALING PROTEIN / Bromodomain / Complex / Inhibitor / Ligand / Halogen bonding / XB / HEFLib / halogen-enriched fragment library
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
3-bromanyl-2~{H}-indazol-5-amine / THIOCYANATE ION / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.202 Å
AuthorsBraun, M.B. / Stehle, T. / Heidrich, J.
CitationJournal: To Be Published
Title: Br-O-modomain (BRD3) halogen binding to a small molecule
Authors: Braun, M.B. / Stehle, S. / Heidrich, J. / Boeckler, F.M.
History
DepositionJan 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,75410
Polymers29,1742
Non-polymers5808
Water4,756264
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9815
Polymers14,5871
Non-polymers3944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7735
Polymers14,5871
Non-polymers1864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.951, 62.071, 84.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bromodomain-containing protein 3 / RING3-like protein


Mass: 14586.843 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059

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Non-polymers , 6 types, 272 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-J58 / 3-bromanyl-2~{H}-indazol-5-amine


Mass: 212.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6BrN3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20 M KSCN, 0.1 M BTPop, 20% PEG3350, 10% EtGly, soaked with 14% DMSO containing 42mM 3-bromo-1H-imidazol-5-amine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.202→43.672 Å / Num. obs: 151382 / % possible obs: 93.6 % / Redundancy: 6.82 % / CC1/2: 1 / Rrim(I) all: 0.04 / Net I/σ(I): 25.48
Reflection shellResolution: 1.202→1.27 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 5.11 / Num. unique obs: 26179 / CC1/2: 0.95 / Rrim(I) all: 0.34 / % possible all: 82.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2nxb

2nxb


Resolution: 1.202→43.672 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.05
RfactorNum. reflection% reflection
Rfree0.16 4553 3.01 %
Rwork0.1409 --
obs0.1414 151378 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.202→43.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 32 264 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012091
X-RAY DIFFRACTIONf_angle_d1.0582846
X-RAY DIFFRACTIONf_dihedral_angle_d15.572804
X-RAY DIFFRACTIONf_chiral_restr0.078298
X-RAY DIFFRACTIONf_plane_restr0.008364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2021-1.21570.18371270.15124097X-RAY DIFFRACTION78
1.2157-1.230.17131290.13544260X-RAY DIFFRACTION82
1.23-1.2450.1821340.13454369X-RAY DIFFRACTION84
1.245-1.26080.13851410.13034411X-RAY DIFFRACTION85
1.2608-1.27740.19751380.12694498X-RAY DIFFRACTION86
1.2774-1.29490.15661400.12234592X-RAY DIFFRACTION87
1.2949-1.31340.13331440.12074601X-RAY DIFFRACTION88
1.3134-1.3330.13511480.11934663X-RAY DIFFRACTION90
1.333-1.35380.1351480.11774768X-RAY DIFFRACTION91
1.3538-1.3760.1381510.11754810X-RAY DIFFRACTION92
1.376-1.39970.1681490.11784801X-RAY DIFFRACTION93
1.3997-1.42520.14551500.11564896X-RAY DIFFRACTION93
1.4252-1.45260.19581490.11244886X-RAY DIFFRACTION93
1.4526-1.48230.13721530.11064920X-RAY DIFFRACTION94
1.4823-1.51450.1321610.10965023X-RAY DIFFRACTION96
1.5145-1.54970.14451520.11025032X-RAY DIFFRACTION97
1.5497-1.58850.14161600.10565080X-RAY DIFFRACTION97
1.5885-1.63140.12971620.10585063X-RAY DIFFRACTION97
1.6314-1.67940.13451550.11075106X-RAY DIFFRACTION98
1.6794-1.73370.14921610.11955123X-RAY DIFFRACTION98
1.7337-1.79560.16851570.12785152X-RAY DIFFRACTION98
1.7956-1.86750.1641550.13245160X-RAY DIFFRACTION98
1.8675-1.95250.14161570.13665188X-RAY DIFFRACTION98
1.9525-2.05540.15611630.13945131X-RAY DIFFRACTION99
2.0554-2.18420.16231620.13925169X-RAY DIFFRACTION99
2.1842-2.35290.15091590.14415193X-RAY DIFFRACTION99
2.3529-2.58960.17131640.15685188X-RAY DIFFRACTION99
2.5896-2.96430.1721610.16435195X-RAY DIFFRACTION100
2.9643-3.73430.16521600.16515213X-RAY DIFFRACTION100
3.7343-43.70050.17621630.15895237X-RAY DIFFRACTION100

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